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Receptor
PDB id Resolution Class Description Source Keywords
4N39 1.76 Å EC: 2.4.1.255 CRYSTAL STRUCTURE OF HUMAN O-GLCNAC TRANSFERASE BOUND TO A P FROM HCF-1 PRO-REPEAT 2 (11-26) HOMO SAPIENS GLYCOSYLTRANSFERASE O-GLCNAC TRANSFERASE PROTEOLYSIS SUBSTDOMAIN TPR BINDING TRANSFERASE-SUBSTRATE COMPLEX
Ref.: HCF-1 IS CLEAVED IN THE ACTIVE SITE OF O-GLCNAC TRA SCIENCE V. 342 1235 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UDP A:1201;
Valid;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6MA3 2 Å EC: 2.4.1.255 CRYSTAL STRUCTURE OF HUMAN O-GLCNAC TRANSFERASE BOUND TO A P FROM HCF-1 PRO-REPEAT 2 (11-26) AND INHIBITOR 2A HOMO SAPIENS OGT O-GLCNAC GLYCOSYLTRANSFERASE ENZYME-INHIBITOR COMPLEXTRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-BASED EVOLUTION OF LOW NANOMOLAR O-GLCNAC TRANSFERASE INHIBITORS. J. AM. CHEM. SOC. V. 140 13542 2018
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4N39 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 6MA3 Kd = 0.005 uM JAJ C28 H27 N3 O9 S2 c1ccc(c(c1....
3 6MA4 Kd = 0.045 uM JA7 C29 H29 N3 O9 S2 c1ccc(c(c1....
4 6MA5 Kd = 0.14 uM J9V C25 H23 N3 O7 S2 COc1ccccc1....
5 6MA2 Kd = 4.1 uM J9S C25 H23 N3 O7 S2 COc1ccccc1....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4N39 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 6MA3 Kd = 0.005 uM JAJ C28 H27 N3 O9 S2 c1ccc(c(c1....
3 6MA4 Kd = 0.045 uM JA7 C29 H29 N3 O9 S2 c1ccc(c(c1....
4 6MA5 Kd = 0.14 uM J9V C25 H23 N3 O7 S2 COc1ccccc1....
5 6MA2 Kd = 4.1 uM J9S C25 H23 N3 O7 S2 COc1ccccc1....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4N39 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 6MA3 Kd = 0.005 uM JAJ C28 H27 N3 O9 S2 c1ccc(c(c1....
3 6MA4 Kd = 0.045 uM JA7 C29 H29 N3 O9 S2 c1ccc(c(c1....
4 6MA5 Kd = 0.14 uM J9V C25 H23 N3 O7 S2 COc1ccccc1....
5 6MA2 Kd = 4.1 uM J9S C25 H23 N3 O7 S2 COc1ccccc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UDP; Similar ligands found: 117
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6MA3; Ligand: JAJ; Similar sites found with APoc: 41
This union binding pocket(no: 1) in the query (biounit: 6ma3.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5ENZ UDP 1.55844
2 4PQG UDP 2.15264
3 1W0O SIA 2.62794
4 5BXA MAN 2.64423
5 2GEK GDP 2.70936
6 1I7E IBS 3.01887
7 5LNE A2G GAL 3.04878
8 3RI1 3RH 3.19489
9 6F5W KG1 3.25203
10 2WTX UDP 3.5865
11 2WTX VDO 3.5865
12 3BEO UDP 3.73333
13 5XVR TRH 3.90625
14 4XSU UDP 4.38144
15 4XSU GLC 4.38144
16 1VGV UD1 4.42708
17 4XJ7 ADE 4.49438
18 1F6D UDP 4.52128
19 2ZUX RAM 4.56853
20 5ZI9 FLC 4.61538
21 3Q3H UDP 4.91284
22 6BTP E8J 4.97512
23 5E5U 1PS 5.02513
24 1RRV TYD 5.28846
25 3OTH TYD 5.33981
26 1WDK N8E 5.38462
27 6EKZ SNP 5.4878
28 2JKG PRO PRO PRO PRO PRO PRO PRO PRO 5.58659
29 3CV3 UDP 5.66502
30 3P4X ADP 5.81114
31 3OTI TYD 6.53266
32 5NV8 TRH 6.66667
33 1ION ADP 7.40741
34 3OKP GDD 7.86802
35 3R7F CP 8.55263
36 5WXK TYD 11.4286
37 1V6A TRE 11.4458
38 3RHZ UDP 13.8643
39 2JLB UDM 17.7817
40 3OKA GDD 19.0476
41 3ZS9 ADP ALF 26.3158
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